SIMCOMP 2.1.4 / SUBCOMP – Chemical Structure Similarity / Chemical Substructure Search

SIMCOMP 2.1.4 /SUBCOMP

:: DESCRIPTION

SIMCOMP (SIMilar COMPound) is a graph-based method for comparing chemical structures. It has been implemented in the KEGG system for searching similar chemical structures in the chemical structure databases.

SUBCOMP (SUBstructure matching of COMPounds) is a bit-string based method for comparing chemical structures. It has been implemented in the KEGG system for searching similar chemical structures in the chemical structure databases, often as a rapid alternative to more time-consuming (but more accurate) SIMCOMP.

::DEVELOPER

Laboratory of Chemical Life Science

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W652-6. doi: 10.1093/nar/gkq367. Epub 2010 May 11.
SIMCOMP/SUBCOMP: chemical structure search servers for network analyses.
Hattori M1, Tanaka N, Kanehisa M, Goto S.

Interference 1.0 – Virtual Knock-out experiments on Biological networks, based on the Centralities Interference notion

Interference 1.0

:: DESCRIPTION

Interference is a Cytoscape plug-in for virtual knock-out experiments on complex networks

::DEVELOPER

The Center for BioMedical Computing (CBMC)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 Interference

:: MORE INFORMATION

Citation

PLoS One. 2014 Feb 20;9(2):e88938. doi: 10.1371/journal.pone.0088938. eCollection 2014.
Node interference and robustness: performing virtual knock-out experiments on biological networks: the case of leukocyte integrin activation network.
Scardoni G, Montresor A, Tosadori G, Laudanna C.

CentiScaPe 2.2 – Centralities for Cytoscape

CentiScaPe 2.2

:: DESCRIPTION

CentiScaPe is a Cytoscape plug-in for calculating network centralities with numerical and graphical output

::DEVELOPER

The Center for BioMedical Computing (CBMC)

:: SCREENSHOTS

::REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 CentiScaPe

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Nov 1;25(21):2857-9. doi: 10.1093/bioinformatics/btp517. Epub 2009 Sep 2.
Analyzing biological network parameters with CentiScaPe.
Scardoni G1, Petterlini M, Laudanna C.

SDREM 1.2 – Signaling and Dynamic Regulatory Events Miner

SDREM 1.2

:: DESCRIPTION

SDREM is a model which integrates static and time series data to link proteins and the pathways they regulate in these networks. SDREM uses prior information about proteins’ likelihood of involvement in a disease (e.g. from screens) to improve the quality of the predicted signaling pathways.

::DEVELOPER

 Systems Biology Group – Carnegie Mellon University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 SDREM

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):i227-36. doi: 10.1093/bioinformatics/btt241.
Identifying proteins controlling key disease signaling pathways.
Gitter A1, Bar-Joseph Z.

Modulerole 1.3.1 – Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks

Modulerole 1.3.1

:: DESCRIPTION

ModuleRole is a user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek.

::DEVELOPER

Guipeng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Modulerole

:: MORE INFORMATION

Citation

PLoS One. 2014 May 1;9(5):e94608. doi: 10.1371/journal.pone.0094608. eCollection 2014.
ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks.
Li G, Li M, Zhang Y, Wang D, Li R, Guimerà R, Gao JT, Zhang MQ.

Argot2 – Functional Annotation of Proteins using the Semantic Similarity in the Gene Ontology

Argot2

:: DESCRIPTION

Argot2 (Annotation Retrieval of Genel Ontology Terms) is able to quickly process thousands of sequences for functional inference. The tool exploits a combined approach based on the clustering process of GO terms dependent on their semantic similarities and a weighting scheme which assesses retrieved hits sharing a certain degree of biological features with the sequence to annotate.

::DEVELOPER

Argot2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S14. doi: 10.1186/1471-2105-13-S4-S14.
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.
Falda M1, Toppo S, Pescarolo A, Lavezzo E, Di Camillo B, Facchinetti A, Cilia E, Velasco R, Fontana P.

COSSY – COntext-Specific Subnetwork discoverY

COSSY

:: DESCRIPTION

COSSY is an algorithm to discover important subnetworks differentiating between two phenotypes (context). It automatically finds differentially expressed subnetworks of closely interacting molecules from molecular interaction networks (such as KEGG or STRING) using gene expression profiles. This is the first non-greedy approach of its kind. COSSY works for any interaction network regardless of the network topology. It can also be used as a highly accurate classification platform.

::DEVELOPER

Data Mining & Information Systems LabTAN LAB

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

COSSY

:: MORE INFORMATION

Citation

Saha A, Tan AC, Kang J.
Automatic context-specific subnetwork discovery from large interaction networks.
PLoS One. 2014 Jan 1;9(1):e84227. doi: 10.1371/journal.pone.0084227. PMID: 24392115; PMCID: PMC3877685.

PATHiWAYS – web-based Signaling Pathway visualization system

PATHiWAYS

:: DESCRIPTION

PATHiWAYS is a web tool for the interpretation of the consequences of the combined changes in expression levels of genes in the context of signaling pathways. Specifically, this tool allows the user to identify the stimulus-response subpathways that are significantly activated or deactivated in the typical case/control experiment. PATHiWAYS identifies all the stimulus-response subpathways of KEGG signaling pathways, calculates the probability of activation of each one, based on the individual gene expression values and identifies those with a significant differential activity between the two conditions compared.

::DEVELOPER

the Computational Biology Unit, at Computational Medicine Institute at CIPF in Valencia, Spain.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W213-7. doi: 10.1093/nar/gkt451. Epub 2013 Jun 8.
Inferring the functional effect of gene expression changes in signaling pathways.
Sebastián-León P1, Carbonell J, Salavert F, Sanchez R, Medina I, Dopazo J.

WaRSwap – Network Motif Discovery

WaRSwap

:: DESCRIPTION

WaRSwap (Weighted and Reverse Swap sampling) is a network randomization method that for the first time provides a practical algorithm for network motif discovery in large multi-layer networks that include Transcription Factors (TFs), microRNAs (miRNAs), and non-TF protein coding genes.

::DEVELOPER

Uwe Ohler’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 WaRSwap

:: MORE INFORMATION

Citation

Genome Biol. 2013 Aug 23;14(8):R85.
Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
Megraw M1, Mukherjee S, Ohler U.

Biocellion 1.2 – Computer Simulation of Living Cell Systems

Biocellion 1.2

:: DESCRIPTION

Biocellion is an agent-PDE (Partial Differential Equation) based simulation framework, designed for solving general models of multicellular biological systems.

::DEVELOPER

Shmulevich Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

 Biocellion

:: MORE INFORMATION

Citation

Biocellion: accelerating computer simulation of multicellular biological system models.
Kang S, Kahan S, McDermott J, Flann N, Shmulevich I.
Bioinformatics. 2014 Jul 26. pii: btu498.